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lib/Bio/Tools/Phylo/PAML/Codeml.pm view on Meta::CPAN
# hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t",
# "S" and "N". If a ML matrix, "lnL" will also be defined. Any
# additional ML parameters estimated by the model will be in an
# array ref under "params"; it's up to the user to know which
# position corresponds to which parameter (since PAML doesn't label
# them, and we can't guess very well yet (a TODO I guess).
printf "The omega ratio for sequences %s vs %s was: %g\n",
$otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega};
# with a little work, these matrices could also be passed to
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lib/Bio/Tools/Run/Alignment/Clustalw.pm view on Meta::CPAN
=head2 TYPE
Title : TYPE
Description : (optional) sequence type: protein or DNA. This allows
you to explicitly overide the programs attempt at
guessing the type of the sequence. It is only useful
if you are using sequences with a VERY strange
composition.
=head2 OUTPUT
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lib/Bio/Tools/Run/Alignment/TCoffee.pm view on Meta::CPAN
my $type = '';
if (! ref $input) {
# check that file exists or throw
$infilename = $input;
unless (-e $input) {return 0;}
# let's peek and guess
open(my $IN,$infilename) || $self->throw("Cannot open $infilename");
my $header = <$IN>;
if( $header =~ /^\s+\d+\s+\d+/ ||
$header =~ /Pileup/i ||
$header =~ /clustal/i ) { # phylip
lib/Bio/Tools/Run/Alignment/TCoffee.pm view on Meta::CPAN
=head2 TYPE
Title : TYPE
Args : [string] DNA, PROTEIN
Description : (optional) set the sequence type, guessed automatically
so should not use this directly
=head2 PARAMETERS
Title : PARAMETERS
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lib/Bio/Variation/IO.pm view on Meta::CPAN
my ($class, %param) = @_;
my ($format);
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
$format = $param{'-format'}
|| $class->_guess_format( $param{-file} || $ARGV[0] )
|| 'flat';
$format = "\L$format"; # normalize capitalization to lower case
return unless $class->_load_format_module($format);
return "Bio::Variation::IO::$format"->new(%param);
lib/Bio/Variation/IO.pm view on Meta::CPAN
my ($self, $seq) = @_;
$self->warn("These are not sequence objects. Use method 'write' instead of 'write_seq'.");
$self->write($seq);
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'flat' if /\.dat$/i;
return 'xml' if /\.xml$/i;
}
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lib/Bio/VertRes/Config/Pipelines/Assembly.pm view on Meta::CPAN
$output_hash->{vrtrack_processed_flags} = { stored => 1, assembled => 0, rna_seq_expression => 0 };
$output_hash->{limits} = $self->_escaped_limits;
$output_hash->{data}{tmp_directory} = $self->_tmp_directory;
# rough guess at the maximum you expect to get
$output_hash->{data}{genome_size} = $self->_genome_size;
$output_hash->{data}{seq_pipeline_root} = $self->root;
$output_hash->{data}{assembler} = $self->_assembler;
$output_hash->{data}{assembler_exec} = $self->_assembler_exec;
$output_hash->{data}{optimiser_exec} = $self->_optimiser_exec;
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inc/Module/AutoInstall.pm view on Meta::CPAN
else {
print
"*** Dependencies will be installed the next time you type '$make'.\n";
}
# make an educated guess of whether we'll need root permission.
print " (You may need to do that as the 'root' user.)\n"
if eval '$>';
}
print "*** $class configuration finished.\n";
inc/Module/AutoInstall.pm view on Meta::CPAN
or _load('CPANPLUS::Shell::Default')
)
);
}
# make guesses on whether we're under the CPAN installation directory
sub _under_cpan {
require Cwd;
require File::Spec;
my $cwd = File::Spec->canonpath( Cwd::cwd() );
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lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm view on Meta::CPAN
Almost all of the following methods MUST be overridden by a
derived class. For some methods there is an implementation here
that assumes "no action" is the right thing, but for many adaptors
this won't be right. There is no way this base implementation can
make any meaningful guesses at the correct values for those.
=cut
=head2 get_persistent_slots
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t/lib/Test/Builder.pm view on Meta::CPAN
details). Returns the reason (ie. the value of $TODO) if running as
todo tests, false otherwise.
todo() is about finding the right package to look for $TODO in. It
uses the exported_to() package to find it. If that's not set, it's
pretty good at guessing the right package to look at based on $Level.
Sometimes there is some confusion about where todo() should be looking
for the $TODO variable. If you want to be sure, tell it explicitly
what $pack to use.
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lib/Bio/Tools/Run/Alignment/Amap.pm view on Meta::CPAN
my ($infilename, $seq, $temp, $tfh);
if (! ref $input) {
# check that file exists or throw
$infilename = $input;
unless (-e $input) {return 0;}
# let's peek and guess
open(IN,$infilename) || $self->throw("Cannot open $infilename");
my $header;
while( defined ($header = <IN>) ) {
last if $header !~ /^\s+$/;
}
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Bio/Align/AlignI.pm view on Meta::CPAN
and RNA. The output is in upper case except when gaps in
a column force output to be in lower case.
Note that if your alignment sequences contain a lot of
IUPAC ambiquity codes you often have to manually set
alphabet. Bio::PrimarySeq::_guess_type thinks they
indicate a protein sequence.
Returns : consensus string
Argument : none
Throws : on protein sequences
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lib/BioX/Seq/Stream.pm view on Meta::CPAN
# handle files coming from different platforms
#my @layers = PerlIO::get_layers($self->{fh});
#binmode($self->{fh},':unix:stdio:crlf');
$self->_guess_format;
$self->_init;
return $self;
lib/BioX/Seq/Stream.pm view on Meta::CPAN
my ($self, $bool) = @_;
$self->{fast} = $bool // 1;
}
sub _guess_format {
my ($self) = @_;
# Filetype guessing must be based on first two bytes (or less)
# which are stored in an object buffer
my $r = (read $self->{fh}, $self->{buffer}, 2);
die "failed to read initial bytes" if ($r != 2);
my $search_path = abs_path(__FILE__);
lib/BioX/Seq/Stream.pm view on Meta::CPAN
if ($classname->_check_type($self)) {
push @matched, $classname;
}
}
die "Failed to guess filetype\n" if (scalar(@matched) < 1);
# uncoverable branch true
die "Multiple filetypes matched\n" if (scalar(@matched) > 1);
eval "require $matched[0]";
bless $self => $matched[0];
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if(@_ < 1){ &HELP_fetch_seq;
}else{
F: for($t=0; $t<@in; $t++){ #'''''''''''' PROMPT ARGV processing ''''''''''''''''''
if($in[$t]=~/^\-c$/i){
$create=1; splice(@in, $t, 1); $t--;
print "\n You should provide database\(e.g, seq.dat\) file with this opt, I guess you did\n";
print "\n If you wanted to make an index with any fasta db, you also have to\n";
print " give the file name. e.g:\n $0 -c /DB/swiss/seq.dat\n";
print " or $0 -c my_db.fa\n\n";
next; }
if($in[$t]=~/^\-af$/){ $fasta=$all=1; splice(@in, $t, 1); $t--; next; }
$name2 = $names2[0];
@str1=split(/\||\,/, $hash1{$names1[0]});
@str2=split(/\||\,/, $hash2{$names2[0]});
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Trying to guess the correct gap char
#_____________________________________________________
if($hash2{$names2[0]}=~/_/){
$gap_chr='_';
}elsif($hash2{$names2[0]}=~/(\W)\W/){
$gap_chr=$1;
if(@your_genome_or_db_to_analyse_file < 1){
print "\n# (E) geanfammer_main: ERROR!\n";
print "\n# Dear $ENV{'USER'}, $0: failed to find input file!\n
Did you put FASTA format DB file as input?\n
Or I guess your INPUT file DOES NOT exist in PWD.\n\n";
print " As like: $0 MG.fa \n\n\n";
print chr(7);
exit;
}
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inc/Module/AutoInstall.pm view on Meta::CPAN
if ( @Missing and not( $CheckOnly or $UnderCPAN ) ) {
require Config;
print
"*** Dependencies will be installed the next time you type '$Config::Config{make}'.\n";
# make an educated guess of whether we'll need root permission.
print " (You may need to do that as the 'root' user.)\n"
if eval '$>';
}
print "*** $class configuration finished.\n";
inc/Module/AutoInstall.pm view on Meta::CPAN
or _load('CPANPLUS::Shell::Default')
)
);
}
# make guesses on whether we're under the CPAN installation directory
sub _under_cpan {
require Cwd;
require File::Spec;
my $cwd = File::Spec->canonpath( Cwd::cwd() );
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#ifndef IVSIZE
# ifdef LONGSIZE
# define IVSIZE LONGSIZE
# else
# define IVSIZE 4 /* A bold guess, but the best we can make. */
# endif
#endif
#ifndef UVTYPE
# define UVTYPE unsigned IVTYPE
#endif
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#ifndef IVSIZE
# ifdef LONGSIZE
# define IVSIZE LONGSIZE
# else
# define IVSIZE 4 /* A bold guess, but the best we can make. */
# endif
#endif
#ifndef UVTYPE
# define UVTYPE unsigned IVTYPE
#endif
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lib/Bit/MorseSignals.pm view on Meta::CPAN
BM_DATA_STORABLE => 2,
};
=head2 C<BM_DATA_AUTO>
Default for non-references messages. Try to guess if the given scalar is an UTF-8 string with C<Encode::is_utf8>.
=head2 C<BM_DATA_PLAIN>
Treats the data as a plain string. No extra mangling in done.
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#ifndef IVSIZE
# ifdef LONGSIZE
# define IVSIZE LONGSIZE
# else
# define IVSIZE 4 /* A bold guess, but the best we can make. */
# endif
#endif
#ifndef UVTYPE
# define UVTYPE unsigned IVTYPE
#endif
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lib/Bitcoin/Crypto/Key/Public.pm view on Meta::CPAN
=head3 get_address
$address_string = $object->get_address()
Returns a string containing the address. Tries to guess which address type is
most fitting:
=over
=item * If the key has a BIP44 purpose set, generates type of address which
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print "It may very well be supported all the way back to ",
format_version(5.003_07), ".\n";
}
else {
print "But given the things $f depends on, it's a good",
" guess that it isn't\n",
"supported prior to ", format_version($todo), ".\n";
}
}
}
}
#ifndef IVSIZE
# ifdef LONGSIZE
# define IVSIZE LONGSIZE
# else
# define IVSIZE 4 /* A bold guess, but the best we can make. */
# endif
#endif
#ifndef UVTYPE
# define UVTYPE unsigned IVTYPE
#endif
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inc/Module/AutoInstall.pm view on Meta::CPAN
if ( @Missing and not( $CheckOnly or $UnderCPAN ) ) {
require Config;
print
"*** Dependencies will be installed the next time you type '$Config::Config{make}'.\n";
# make an educated guess of whether we'll need root permission.
print " (You may need to do that as the 'root' user.)\n"
if eval '$>';
}
print "*** $class configuration finished.\n";
inc/Module/AutoInstall.pm view on Meta::CPAN
or _load('CPANPLUS::Shell::Default')
)
);
}
# make guesses on whether we're under the CPAN installation directory
sub _under_cpan {
require Cwd;
require File::Spec;
my $cwd = File::Spec->canonpath( Cwd::cwd() );
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* capable of those should have IVSIZE already. */
#if !defined(IVSIZE) && defined(LONGSIZE)
# define IVSIZE LONGSIZE
#endif
#ifndef IVSIZE
# define IVSIZE 4 /* A bold guess, but the best we can make. */
#endif
#ifndef UVSIZE
# define UVSIZE IVSIZE
#endif
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inc/Module/AutoInstall.pm view on Meta::CPAN
if ( @Missing and not( $CheckOnly or $UnderCPAN ) ) {
require Config;
print
"*** Dependencies will be installed the next time you type '$Config::Config{make}'.\n";
# make an educated guess of whether we'll need root permission.
print " (You may need to do that as the 'root' user.)\n"
if eval '$>';
}
print "*** $class configuration finished.\n";
inc/Module/AutoInstall.pm view on Meta::CPAN
or _load('CPANPLUS::Shell::Default')
)
);
}
# make guesses on whether we're under the CPAN installation directory
sub _under_cpan {
require Cwd;
require File::Spec;
my $cwd = File::Spec->canonpath( Cwd::cwd() );
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inc/Module/AutoInstall.pm view on Meta::CPAN
if ( @Missing and not( $CheckOnly or $UnderCPAN ) ) {
require Config;
print
"*** Dependencies will be installed the next time you type '$Config::Config{make}'.\n";
# make an educated guess of whether we'll need root permission.
print " (You may need to do that as the 'root' user.)\n"
if eval '$>';
}
print "*** $class configuration finished.\n";
inc/Module/AutoInstall.pm view on Meta::CPAN
or _load('CPANPLUS::Shell::Default')
)
);
}
# make guesses on whether we're under the CPAN installation directory
sub _under_cpan {
require Cwd;
require File::Spec;
my $cwd = File::Spec->canonpath( Cwd::cwd() );
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lib/Bolts/Inference/Moose.pm view on Meta::CPAN
=head1 DESCRIPTION
Performs inferrence for L<Moose> object constructor injection on
L<Bolts::Blueprint::Factory>. That is, it is the way in which Bolts will
automatically guess how to build your Moose objects, provided you construct them
with L<Bolts::Blueprint::Factory> (see the L</SYNOPSIS> for an example).
This works by iterating through the attributes on the metaclass for the Moose
object set on the L<Bolts::Blueprint::Factory/class> of the blueprint. If the
attribute has an C<init_arg> set (which all do by default to a name matching the
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lib/Bone/Easy/Rules.pm view on Meta::CPAN
POWEROF-->MYBODYPART
INQUIREZ-->ask me
INQUIREZ-->tell me
INQUIREZ-->guess
INQUIREZ-->decide
INQUIREZ-->think about
INQUIREZ-->imagine
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lib/Bookmarks/Parser.pm view on Meta::CPAN
Parse a collection of bookmarks. This can be passed a filename of a bookmarks
file on a local disk, or a url and user/passwd combination of a bookmarks
collection stored on a remote server.
Currently, best guesses are made as to which type of bookmarks collection is
being parsed, Opera, Netscape/Mozilla and Delicious are supported so far.
=head2 set_title (method)
Parameters:
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src/boost/cstdint.hpp view on Meta::CPAN
namespace boost
{
// These are fairly safe guesses for some 16-bit, and most 32-bit and 64-bit
// platforms. For other systems, they will have to be hand tailored.
//
// Because the fast types are assumed to be the same as the undecorated types,
// it may be possible to hand tailor a more efficient implementation. Such
// an optimization may be illusionary; on the Intel x86-family 386 on, for
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Directed/ppport.h view on Meta::CPAN
* capable of those should have IVSIZE already. */
#if !defined(IVSIZE) && defined(LONGSIZE)
# define IVSIZE LONGSIZE
#endif
#ifndef IVSIZE
# define IVSIZE 4 /* A bold guess, but the best we can make. */
#endif
#ifndef UVSIZE
# define UVSIZE IVSIZE
#endif
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bootylicious view on Meta::CPAN
%#
%# This configuration is in JSON format, that is preprocessed by Mojo::Template.
%# Yes, you can use Perl here.
{
%# Change this to something not guessable
%# "secret" : "Unique string",
%# Blog description settings
%# "author" : "whoami",
%# "email" : "",